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Crystallographic structure of a feruloyl esterase from Aspergillus niger
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 4TGL PDB ENTRY 4TGL
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 4.5 1.0 M AMMONIUM SULPHATE, 0.1M NA ACETATE PH 4.5
Crystal Properties Matthews coefficient Solvent content 1.8 32
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 38.298 α = 75.24 b = 39.681 β = 78.82 c = 77.071 γ = 71.3
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 M
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID14-2 ESRF ID14-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 1.5 25 94.4 0.06 11.5 2.1 64076 14.8
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 1.51 1.53 95.3 0.17 2.5 1.8
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 4TGL 1.5 74.54 64009 3252 96.8 0.158 0.156 0.1656 0.188 0.1952 RANDOM 13.53
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.131 0.122 0.318 0.988 0.137 -1.128
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.612 r_dihedral_angle_3_deg 12.886 r_dihedral_angle_4_deg 11.628 r_dihedral_angle_1_deg 6.035 r_scangle_it 3.829 r_scbond_it 2.915 r_angle_refined_deg 1.766 r_mcangle_it 1.732 r_mcbond_it 1.388 r_angle_other_deg 0.965
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 38.612 r_dihedral_angle_3_deg 12.886 r_dihedral_angle_4_deg 11.628 r_dihedral_angle_1_deg 6.035 r_scangle_it 3.829 r_scbond_it 2.915 r_angle_refined_deg 1.766 r_mcangle_it 1.732 r_mcbond_it 1.388 r_angle_other_deg 0.965 r_nbd_refined 0.229 r_nbd_other 0.202 r_symmetry_vdw_other 0.198 r_symmetry_hbond_refined 0.194 r_nbtor_refined 0.189 r_symmetry_vdw_refined 0.188 r_xyhbond_nbd_refined 0.144 r_chiral_restr 0.126 r_nbtor_other 0.09 r_bond_refined_d 0.019 r_gen_planes_refined 0.009 r_bond_other_d 0.005 r_gen_planes_other 0.001 r_xyhbond_nbd_other r_metal_ion_refined r_metal_ion_other r_symmetry_hbond_other r_symmetry_metal_ion_refined r_symmetry_metal_ion_other r_mcbond_other r_mcangle_other r_scbond_other r_scangle_other r_long_range_B_refined r_long_range_B_other r_rigid_bond_restr r_sphericity_free r_sphericity_bonded
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 3978 Nucleic Acid Atoms Solvent Atoms 398 Heterogen Atoms 38
Software Software Software Name Purpose REFMAC refinement DENZO data reduction SCALEPACK data scaling AMoRE phasing